LAMMPS (27 Jun 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file

# run the first part and write out restart
include in.molecular-mix
# demo for atom style template simulating a cyclohexane methane mixture

units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
LAMMPS molecule file. Cyclohexane(UA)
  1 molecules
  0 fragments
  6 atoms with max type 1
  6 bonds with max type 1
  6 angles with max type 1
  6 dihedrals with max type 1
  0 impropers with max type 0
atom_style molecular

pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic

lattice sc 6.0
Lattice spacing in x,y,z = 6 6 6
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6                  extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2
Created orthogonal box = (-24 -24 -24) to (24 24 24)
  1 by 1 by 1 MPI processor grid

create_atoms 0 box mol cychex 734594
Created 3072 atoms
  using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
  create_atoms CPU = 0.004 seconds
create_atoms 2 random 800 495437 box
Created 800 atoms
  using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
  create_atoms CPU = 0.000 seconds

mass 1 14.027
mass 2 16.043

pair_coeff 1 1  0.1180  3.905
pair_coeff 2 2  0.2940  3.730

bond_coeff      1  260.00 1.5260
angle_coeff     1  63.0   112.40
dihedral_coeff  1  2.0 1 3

thermo 100
minimize 0.001 0.001 500 1000
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 7 7 7
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.28 | 12.28 | 12.28 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0              4.3897851e+13  341.92144      4.3897851e+13  1.0886888e+14
       100   0             -4351.8383      516.49891     -3835.3394      11635.037    
       190   0             -6191.8196      457.61266     -5734.2069      4365.4279    
Loop time of 2.5667 on 1 procs for 190 steps with 3872 atoms

99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = energy tolerance
  Energy initial, next-to-last, final = 
      43897850768892.8  -5729.17409504969  -5734.20694761353
  Force two-norm initial, final = 1.1080994e+15 72.745546
  Force max component initial, final = 4.6607099e+14 17.390179
  Final line search alpha, max atom move = 0.0041638487 0.072410076
  Iterations, force evaluations = 190 297

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 2.2379     | 2.2379     | 2.2379     |   0.0 | 87.19
Bond    | 0.070658   | 0.070658   | 0.070658   |   0.0 |  2.75
Neigh   | 0.21093    | 0.21093    | 0.21093    |   0.0 |  8.22
Comm    | 0.012111   | 0.012111   | 0.012111   |   0.0 |  0.47
Output  | 3.0458e-05 | 3.0458e-05 | 3.0458e-05 |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.03504    |            |       |  1.37

Nlocal:           3872 ave        3872 max        3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          12122 ave       12122 max       12122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         774375 ave      774375 max      774375 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 774375
Ave neighs/atom = 199.99354
Ave special neighs/atom = 3.9669421
Neighbor list builds = 14
Dangerous builds = 0
reset_timestep 0

velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 11.16 | 11.16 | 11.16 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   100           -6191.8196      457.61266     -4580.3354      4842.371     
       100   106.81292     -5670.2785      921.2043      -3516.5903      5959.4321    
       200   119.24063     -5701.0127      1040.0231     -3285.1059      6755.2619    
       300   127.28216     -5706.3887      1026.2838     -3211.4322      6076.6123    
       400   133.79038     -5734.0279      1113.6088     -3076.65        6583.9393    
       500   138.77685     -5756.2532      1192.1349     -2962.8117      6436.3524    
       600   149.39857     -5730.563       1206.6372     -2800.0582      6357.5889    
       700   155.5825      -5671.0161      929.50406     -2946.2899      7697.5164    
       800   161.24677     -5628.3833      1186.5533     -2581.2493      5840.6503    
       900   172.81747     -5638.6453      1148.683      -2495.8707      8169.3352    
      1000   182.2048      -5579.5767      909.90783     -2567.2594      6270.7354    
      1100   188.95766     -5548.999       1183.6644     -2185.0058      7711.9244    
      1200   195.22147     -5511.6798      1111.3361     -2147.7386      7656.4439    
      1300   205.15867     -5431.6966      1195.8143     -1868.6148      7021.8716    
      1400   211.44641     -5410.5687      1299.0501     -1671.6986      8903.0061    
      1500   223.70124     -5359.4567      1388.4189     -1389.8128      6919.2408    
      1600   231.75318     -5288.3343      1348.829      -1265.3712      9409.2728    
      1700   229.61746     -5259.4318      1194.5663     -1415.375       7387.4923    
      1800   245.62483     -5281.0755      1389.3362     -1057.5441      9421.7241    
      1900   250.69445     -5158.7006      1236.5167     -1029.4919      8649.4835    
      2000   259.50657     -5148.4153      1485.1392     -668.90355      9130.4701    
      2100   270.77108     -5092.6634      1418.7937     -549.51913      9666.5632    
      2200   272.30152     -5079.7585      1514.5708     -423.17779      8568.2546    
      2300   285.20945     -5085.6197      1492.5671     -302.10191      10281.574    
      2400   286.95799     -4979.8608      1544.6159     -124.11819      8797.7435    
      2500   296.10218     -4928.5152      1698.282       186.40572      10946.864    
Loop time of 17.2353 on 1 procs for 2500 steps with 3872 atoms

Performance: 12.532 ns/day, 1.915 hours/ns, 145.052 timesteps/s, 561.639 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 15.936     | 15.936     | 15.936     |   0.0 | 92.46
Bond    | 0.5636     | 0.5636     | 0.5636     |   0.0 |  3.27
Neigh   | 0.51213    | 0.51213    | 0.51213    |   0.0 |  2.97
Comm    | 0.098127   | 0.098127   | 0.098127   |   0.0 |  0.57
Output  | 0.00072478 | 0.00072478 | 0.00072478 |   0.0 |  0.00
Modify  | 0.10177    | 0.10177    | 0.10177    |   0.0 |  0.59
Other   |            | 0.02248    |            |       |  0.13

Nlocal:           3872 ave        3872 max        3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          11821 ave       11821 max       11821 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         770416 ave      770416 max      770416 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 770416
Ave neighs/atom = 198.97107
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0
#write_data molecular-mix.data
#write_restart molecular-mix.restart
write_restart molecular-mix.restart
System init for write_restart ...
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule

# now restart
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
molecule cychex cyclohexane.mol
Read molecule template cychex:
LAMMPS molecule file. Cyclohexane(UA)
  1 molecules
  0 fragments
  6 atoms with max type 1
  6 bonds with max type 1
  6 angles with max type 1
  6 dihedrals with max type 1
  0 impropers with max type 0
read_restart molecular-mix.restart
Reading restart file ...
  restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024
  restoring atom style molecular from restart
  orthogonal box = (-24 -24 -24) to (24 24 24)
  1 by 1 by 1 MPI processor grid
  restoring pair style lj/cut from restart
  restoring bond style harmonic from restart
  restoring angle style harmonic from restart
  restoring dihedral style harmonic from restart
  3872 atoms
  3072 bonds
  3072 angles
  3072 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     2 = max # of 1-2 neighbors
     2 = max # of 1-3 neighbors
     4 = max # of 1-4 neighbors
     7 = max # of special neighbors
  special bonds CPU = 0.001 seconds
  read_restart CPU = 0.003 seconds

thermo 100

fix 1 all nvt temp 300.0 300.0 1.0
Resetting global fix info from restart file:
  fix style: nvt, fix ID: 1
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
All restart file global fix info was re-assigned
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 7 7 7
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.12 | 11.12 | 11.12 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
      2500   296.10218     -4928.5152      1698.282       186.40572      10946.864    
      2600   302.98473     -4910.6997      1585.9276      171.28257      9066.357     
      2700   300.75989     -4935.1005      1723.6514      258.9337       10755.67     
      2800   294.26086     -4904.3072      1594.9394      86.02469       9420.9997    
      2900   296.15059     -4961.5041      1594.1004      49.793724      10129.823    
      3000   296.65334     -4934.6622      1596.9704      85.306731      10112.636    
      3100   301.62361     -4975.5261      1671.8512      176.67422      9500.7576    
      3200   297.34385     -5017.986       1603.4388      16.419054      10451.2      
      3300   297.01108     -4882.1137      1651.6426      196.65525      9124.096     
      3400   298.13642     -4983.4532      1742.3589      199.01715      10808.599    
      3500   315.91146     -4952.209       1651.2231      344.22669      8677.2632    
      3600   295.12433     -4950.6158      1721.3273      176.06725      10904.222    
      3700   300.65909     -4967.4001      1770.4243      272.244        9230.4292    
      3800   302.15034     -4991.9549      1644.8366      139.30847      10154.524    
      3900   302.16277     -5017.0117      1672.2353      141.79397      9705.6697    
      4000   303.1458      -4946.2517      1679.8498      231.51137      9527.8793    
      4100   303.54737     -5003.8276      1639.7221      138.44129      10406.442    
      4200   291.62491     -5009.3438      1707.6         63.233087      8645.4116    
      4300   306.17115     -5084.7139      1727.9528      176.0607       10563.216    
      4400   302.65581     -5004.4302      1747.5309      235.36003      8717.1253    
      4500   296.42334     -5014.9791      1723.2084      128.57389      10492.246    
Loop time of 13.288 on 1 procs for 2000 steps with 3872 atoms

Performance: 13.004 ns/day, 1.846 hours/ns, 150.512 timesteps/s, 582.781 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 12.191     | 12.191     | 12.191     |   0.0 | 91.74
Bond    | 0.4224     | 0.4224     | 0.4224     |   0.0 |  3.18
Neigh   | 0.50894    | 0.50894    | 0.50894    |   0.0 |  3.83
Comm    | 0.07309    | 0.07309    | 0.07309    |   0.0 |  0.55
Output  | 0.00057158 | 0.00057158 | 0.00057158 |   0.0 |  0.00
Modify  | 0.077778   | 0.077778   | 0.077778   |   0.0 |  0.59
Other   |            | 0.01451    |            |       |  0.11

Nlocal:           3872 ave        3872 max        3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          11685 ave       11685 max       11685 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         770346 ave      770346 max      770346 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 770346
Ave neighs/atom = 198.953
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0

# clean up
shell rm molecular-mix.restart
Total wall time: 0:00:33
